scottie wrote:You will not find that I have anywhere, said that nor have I made any such accusation. I appreciate you used the word “believe” which only goes to show that beliefs can be wrong.

I'm too lazy to plough through your posts to find where I was led to my belief. Either I am mistaken, or you have not taken enough care in expressing yourself. The rest of my last post, however, remains as it is.

Let me briefly summarize my subjective perception of the situation here. Unless I am biased, the biggest counter argument to Scottie’s claims about improbability of the randomness’ role in the processes described over the last 32 pages is absence of any evidence that supports existence of the supernatural “intelligent agency” that Scottie keeps referring to. Am I correct?

Thanks for your interjection, it’s nice to have a fresh view presented.

Firstly could we nail down this point. The introduction of vestigial organs is an argument for degeneration in an already existing function, whatever the cause of that degeneration.It does not stand up as an argument against functional design.

However canalon and now you both make the same point about essentially keeping up with new information as this is the way science proceeds. You also say that old information isn’t necessarily outdated or wrong. I completely agree. However simply reading reviews does not advance your knowledge of a subject. Reading the papers themselves is what matters and that is what I encourage you to do.

So let examine what the latest papers are revealing about evidence on this subject.Of necessity this post will be somewhat long, because in science the detail of evidence is important.

It is still not known how cave fish have lost eyesight and pigmentation. This is not just my view.

Today, the mystery still persists, although the field of possibilities has been narrowed to two opposing hypotheses… The neutral mutation hypothesis (Kimura and Ohta 1971) suggests that eye regression is caused by random mutations in eye-forming genes, which accumulate in cave animals under relaxed selective pressure

Remember this is the hypothesis that Professor Deamer offered in1964.Jeffery continues.

In contrast, the adaptation hypothesis suggests that loss of eyes is adaptive and has a selective advantage in the cave environment (Culver 1982; Poulson 1963;Poulson and White 1969). As implied in the Darwin quote, however, the actual benefits of blindness have been difficult to understand.

This hypothesis is the one favoured by Jeffrery along with others, and is a Darwinian explanation.

Jeffery summarises the very interesting discoveries in the molecular changes that take place during this process. (new information) The paper is a fascinating read.

Eye formation does commence in the embryo but is arrested at a certain stage in development. ( Deamer in 1964 referred to Vandel’s (1961) discovery of this fact.)

This arresting takes place during lens formation. However no genes understood to function during eye formation, appear to be damaged. Also when the lens of an embryo of a surface fish is transplanted into the embryo of a cave fish at the same stage development the eye in the cave fish continues to develop normally. When a reverse transplant takes place the eye of the surface embryo is arrested, suggesting that the lens is the central controller of eye formation.

It has also been discovered that many genes are up regulated in cavefish relative to surface fish, rather than vice versa. The expanded regulation in particular of the hh genes seems to be quite central in the degenerative process. It is for these reasons that Jeffery hypothesises that Natural selection is at work and not mutation.

Surface ﬁsh and caveﬁsh brains are remarkably different, much more than expected from phenotypic variation within the same species. Page 270 2nd column…The evolutionary forces that generate these changes are not understood. …page 271 1st columnHow and why behavioral changes have evolved is almost completely uncharted territory.The relative simplicity of caveﬁsh behaviors may reﬂect the short time since their original divergence, underscoring the importance of a micro evolutionary perspective. Astyanax has the potential to make signiﬁcant contributions to understanding the evolution of behavior at the molecular level.

Therefore, it is likely that in cave ﬁsh with a transplanted lens from surface ﬁsh the retina remained in its reduced state characteristic of other cave ﬁsh. This result is supported by the observation that these specimens did not respond to light (Romero et al., 2003). This ﬁnding suggests that for the restoration of an eye two subunits, lens and retina, would be necessary. Thus the ‘complete restoration of the eye’ as hypothesised by Jeffery (2005) has not been shown and hence there is no support for the hypothesis that the lens alone has a ‘central role in cave ﬁsh eye development’.

Thus, I suggest that eye regression in Astyanax seems to be mainly because of down regulation of structural genes by the expanded hh gene expression,which was suggested to have a causal role in eye development of the cave ﬁsh (Yamamoto et al., 2004).However, the question of what causes downregulation of hh genes remains unsolved.

Keeping in mind that expanded expression of the hh genes may have a causal role in eye reduction of the parental cave ﬁsh, the development of ‘back to surface eyes’ could be explained by the secondary restriction of expression and downregulation of hh genes. I suggest that this could be due to as yet unidentiﬁed genes. In contrast to the hh genes, it is likely that these genes show loss-of-function mutations. In ‘back to surface eyes’ they could be expressed again because of the complementary restitution of their function.

I suggest that the variability of regressive traits is attributed to the loss of selection. Explanations of the reduction of biologically functionless traits in cave ﬁsh based on selection seem to be less probable because natural selection usually acts strongly to eliminate phenotypic variability. Therefore, variability of regressive traits in cave animals would be one of the rare cases, in which random mutations can manifest and are not eliminated by natural selection acting to preserve the functional capability of a module.

Both the eyeless epigean fish and cave fish with induced eyes are indifferent to the illumination whereas the surface forms are scotophilic, suggesting that optic development and phototactic behavior are decoupled.

So despite the passing of nearly 50 years Professor Deamer’s hypothesis is still very much in alive and kicking.

The last point I make is this.Jefferies (2008) makes good mention of cave fish as being a natural lab for the study of evolution since here we have both ancestor (suface) fish and their descendents (cave fish)Also note that he recognises this process as micro evolution (variation within a species)

Now lets return to Deamer’s reference to (Woods1956) the evidence from which can be downloaded here. http://libsysdigi.library.uiuc.edu/OCA/Books2008 08/bulletin1/bulletin25chic/bulletin25chic.pdfCHICAGO NATURAL HISTORY MUSEUM BULLETIN November 1954 page 4

Here is first hand evidence of the gradation of this degeneration that Deamer used to support his hypothesis. Evidence from the natural habitat.

Another kind well-known to aquarists is the cave tetra from San Luis Potosi, Mexico. This species reveals a fourstep gradation in the degeneration of the eyes from perfectly eyed, normally pigmented, surface-dwelling individuals to totally blind ones with the eye socket covered with tissue and no evident eye structure

So it is from the evidence of the natural environment that Deamer claims support for his view. Even today we are unable to identify the actual theoretical mechanism of natural selection at work.How does Jeffery he put it?

The evolutionary forces that generate these changes are not understood

If even within micro evolution (which as far as I know everyone accepts) natural selection cannot be identified at work, how is it that the Darwinian process of macro evolution is so certainly propounded as fact?

Therefore and with great respect, I would encourage both you and canalon to keep away from sweeping statements, unless you are confident you can back them up with evidence.btw I have not yet received a reply from Professor Deamer. It is after all the holiday period.

Scottie, I view your arguments and the data you present as very convincing, logical and informative. Also, as I already said, I applaud the effort you applied to learn the subject not immediately relevant to your specialization, and the bravery with which you battle your powerful opposition. Unfortunately, until the detailed explanation is provided about what the “intelligent agency” actually is and by what means it acts on the natural world, I am afraid that the case you present will remain a topic of a casual conversation, but not a scientific symposium. I don’t see how it can be easily done to satisfy the scientific method though.

This conversation is a flexing of intellectual muscle, not more, not less. It reminds me a ball set in motion in a U-shaped jar. The ball keeps moving in opposite directions driven by the gravity of opposing arguments, but at the end it is really not going anywhere. An intellectually advanced debater can always BS his way out of any situation because reductionist approach to the complexity of life (which has been billions of years in existence by now) can spawn a countless number of explanations. And when the conversation hits dead end, one can always say that the source of the genomic toolkit (and all the mechanisms around it) has either dissolved in Precambrian period without a trace, or will be explained sometime in the future or is hiding in the world beyond the realm of Physics.

Now the soft-bodied creatures being dissolved, people understand. But there will always be an issue with “selling” the idea of a “super intellectual agency”. I, personally, don’t have a huge problem to make a “leap of faith” to agree with you. But as a former hardcore atheist, I see where your opponents are coming from. However, I do hope the thread will continue its existence, cause it tackles with very important issues of philosophical nature. After all, I am not really sure if I truly care about all of these if at the end our fellow C. elegans will feast on my neatly mapped genome, poop it out, and that will be pretty much the end of this story.

Sorry for the delay is responding.I deliberately took a couple of days away from the forum just to unfreeze my brain cells. Also to give those who are disposed to reading the papers I refer to, have a chance to digest them.

I very much appreciate your comments though.

When I entered this thread back in April I made this point.

Now I don't get hung up on terminology. When I see design I see it for what it is –Design. I don't need to prefix it with adjectives such as “Intelligent” as the ID community does or “Apparent” as Richard Dawkins does.

How did this design come about? Well I don't see this has been answered by science. We haven't even been able to explain what life is so how can science know how it came about. If it came about by supernatural means then science will never be able to answer it.

Science however can explain how it could not have come about.

I have remained consistent on this subject, simply because it is part of my belief system, i.e. the scientific method. From the evidence produced I form my conclusions.The evidence from science clearly shows me that life could not have got started by any known natural process.The evidence also shows, through advances in molecular biology, random mutations of a genome cannot produce the functional design we all see in life processes and this is why Darwinism does not explain these life processes.

What I have found in any philosophical dogma, is that sooner or later contradictions set in.This is so exemplified in this cave animal vestigial and Junk DNA argument.

Here we have a theory that, at it’s core, describes a process of random mutations of a genome eventually producing function, that another process, natural selection, filters to conserve one particular function, for survival.

In the case of cave animals however the precise reverse is being argued. Why?The reason it seams to me, is to try and preserve natural selection as the filter. We know that these cavefish (for example) are the same species as their surface relatives. They can interbreed, and yet they are arguing mutation has not caused the difference, even though it was the initial cause of the species arriving in the first place. Remember also cave animals are ubiquitous in nature, so this is not some freak happening.

How can a theory so successfully contradict itself and the adherents not see it?I find this quite astonishing. My only answer to that question is,-- the theory is a philosophical view and not a scientific one.

I understand the point you are trying to make when you say:-

Unfortunately, until the detailed explanation is provided about what the “intelligent agency” actually is and by what means it acts on the natural worldI am afraid that the case you present will remain a topic of a casual conversation, but not a scientific symposium. I don’t see how it can be easily done to satisfy the scientific method though.

With respect I have to disagree with you. It is the scientific method that is falsifying the fundamental tenets of evolutionary theory. Its promoters claim it to be genuine science, therefore it should be judged by the scientific method.

However is the scientific method falsifying design by an outside agency? It is certainly not falsifying the design argument, so that leaves the “outside agency” bit.

Now if, by argument the case is as you are implying, that an actual description of the agency must be supplied for it to be treated scientifically, then there should be consistency in this argument for both sides.So does the theory or indeed any evolutionary scientist know what the common ancestor, sitting at the base of the TOL is or was?Ok let’s make it easier.Does the theory or any scientist describe the common ancestor of the human/ape lineage, or the common ancestor of the bear/panda lineage?I know what the answer is.

Junk DNA was used as proof of evolutionary theory. Now as it has become clear that these areas are in fact very much functional most are simply burying their heads in the sand or trying to find ways to show how it does in fact support evolutionary theory.So no matter what the evidence, it supports evolution. Sounds very philosophical to me and certainly not scientific.

I would like to post some more information on what the latest research is revealing on mouse, rats and humans, but that had better wait for the moment.

I can't figure out why you're still going on about this, scottie. You believe in the Creator Thing and others do not. Science cannot prove or disprove its existence. Your "disproofs" of evolution are (embarrassingly) feeble compared to the weight of evidence in its support. The only people who do not support evolution are those who are ignorant of the evidence and those who WANT to believe in something else. The lack of scientific proof of a natural cause of whatever does NOT LOGICALLY LEAD to the existence of a Creator Thing. You are CHOOSING to believe in it, because you apparently WANT it to exist, not because any great body of evidence supports its existence or fails to support a naturalistic explanation. So why are you devoting so much time and effort to this thread? It's very apparent that you must be spending HUGE amounts of time on this project, but I can't for the life of me figure out what your project is. Are you on a personal quest to convince one part of your brain of something that another part refuses to accept? Or what. exactly?

Gavin, here is your statement: “The only people who do not support evolution are those who are ignorant of the evidence…”And here is definition of evolution: “Evolution is any change across successive generations in the heritable characteristics of biological populations.” (Wiki)

Now, I may have a serious problem with my English, cause I haven’t noticed here anything that would’ve contradicted the abovementioned description of evolution. The label of “evolution denier” is frequently used just like a “holocaust denier” and people rarely bother to explain what they actually mean by that. If Scottie questioned the randomness role behind genetic or epigenetic complexity / abiogenesis or saltation, then I still don’t see what exactly the evidence you are talking about is. Perhaps I have to admit my ignorance (and I already did that) and acquire a PhD in biology to see your point? But here is the dilemma - I’ve never seen anyone questioning the validity of the Pythagorean theorem, but I saw PhD-s clashing over the randomness as one of the key elements of the evolution from the first amino acid to a man. So maybe it’s not ignorance that causing the issues here… Maybe the only possible alternative to randomness - supernatural involvement being that, is causing the controversy…

On a personal note… One time I ran into event, 2 degrees later, I have absolutely no natural explanation to. What was it is irrelevant and it didn’t really prove anything specific, but it has absolutely reshuffled the weights I allocated to the elements in the equation of my perception of reality. Putting aside charlatanism, circus tricks, and misunderstood natural phenomenon, the supernatural to me is no longer multiplied by zero. Now I view it as being relevant to some form of rare phenomenon superior to our level of knowledge & superior to our ability to readily sense and perceive the reality from which it originated.

Let me mention the quote C. Venter is credited with: “…we are literally coming out of the dark ages of biology. As a civilization, we know far less than one per cent of what will be known about biology, human physiology, and medicine. My view of biology is 'We don't know s*%t.' "http://www.mindfully.org/GE/Venter-Genome-Warrior12jun00.htmI would rephrase him in a broader sense – we still don’t know s*%t about reality that surrounds us. We’re all balancing on the scales of our believes systems, and direction in which the scales tip depends a lot on our personal experiences. The scientific method helps us to objectively filter out mumbo-jumbo portion of these experiences, but I’m afraid the limitations of our sensory capabilities sometimes impair it severely, feeding the believes in impossibility of something that might as well be possible.

I can only repeat what I already said – I’m not qualified to embrace Scotties case, but I don’t see any grounds to firmly reject it except the ones rooted in some form of religious atheism (and ignorance doesn’t seem to be a part of the picture here). Maybe if his arguments were predominantly discussed and judged on their own merits, the discussion would be more beneficial.

I am not trying to get anyone to believe in the “Creator thing” as you call it.What I am trying to do is put my understanding of science (biology in this case) to the test regarding the purpose of this thread. “Theories – Origin of life”.

Your "disproofs" of evolution are (embarrassingly) feeble compared to the weight of evidence in its support.

I can only point to the evidence that supports my understanding. If the “weight of evidence” as you put it supports your position then surely my feeble disproof’s should be easily countered with evidence. Remember you did try, when you took up my challenge to reveal what would falsify “neo Darwinism”.

The weight of evidence does pile up in favour of the concept of micro evolution, which of course is variation within species. But this discussion is about more. Darwin’s whole view was about speciation, not variation within species. Now you have quite clearly stated that you prefer to accept the mechanism of variation within species to extend across to producing new species.I don’t see that evidence and post accordingly. This is a perfectly acceptable scientific position to take.For philosophical reasons you choose to disagree. I certainly don’t have a problem with that, in fact I commend you and indeed have done for being honest enough to acknowledge that.You are also correct

The lack of scientific proof of a natural cause of whatever does NOT LOGICALLY LEAD to the existence of a Creator Thing.

Is it not also the case that functional design can lead logically to a designer.In the end it boils down to the scientific evidence, and that is where I am coming from.

I am passionate about science, I also have enough time and inclination to delve into the subject and bore every one silly with my findings.

I believe Nick7 makes a valid point when he says

I don’t see any grounds to firmly reject it except the ones rooted in some form of religious atheism

You have acknowledged this but others have chosen to engage in rhetoric rather than produce evidence which stacks up.

If evolutionary theory is correct then I will readily endorse it. Put me to the test.

Do keep in mind that there are many religious people who endorse the Darwinian process.

Just go to the BioLogos Foundation site started by Francis Collins who is one of the top geneticists and headed the Human Genome Project, and is now Director of the National Institutes of Health

This is being made into a religious issue. Why?Darwinism is not the sole prerogative of atheism.

You see design in nature and argue that there must be a designer (a bit tautological, that). By accepting design as a given, you cannot lay any claim to scientific rigour. Science must assume that supernatural forces are not responsible for whatever is being studied. Science does not (cannot) rely on proof, just probability based on the available evidence. The available evidence does not lean toward any design in nature. Design is a preconception, not an observation. You can believe whatever you want, but please don't try to claim that science supports your beliefs. You may be passionate about what you think science is, but cherry-picking in science leads to bad science. All scientists plough through the literature trying to find support for their pet theories, but they cannot ignore the findings that contradict their theories. Please don't dismiss evidence that doesn't support what you want to be true. Doing so doesn't make it true. And is not good science.

You see design in nature and argue that there must be a designer (a bit tautological, that).

That is an interesting statement.But trying to move the goal posts into the philosophical area won’t work, and for this reason.

You could have a case if I did not define how my argument for functional design could be falsified.However I have done precisely that, and it is about where you entered into this discussion. Remember!

scottie » Tue Jun 21, 2011 10:20 pm

To be regarded as science then it must be falsifiable. So once again, is this understanding falsifiable?I answer Yes, it can be falsified, and there is nothing “secretive” about this.

Every one is aware that functional design (whether good, or not so good or even downright bad) displays itself with certain properties.1) The function has a purpose. ( i.e. It goes from A to B with C as it’s goal )2) Method by which that purpose is achieved. (How does it go from A to B)3) It would not contain parts or units that had no function toward the purpose.

Therefore, falsifying this hypothesis would require that parts of the genome were non functional. Now if that was the case then that would be an argument against my hypothesis.

So, all you have to do provide evidence that any part(s) of the genome are non functional and my hypothesis is in trouble.There you are, I have told you what you need to show.Should be quite simple, shouldn’t it?

Now you tried to falsify and failed with the phylogenetic data and tree building.. argument

However where have you or indeed anyone even attempted to define how Darwinism could be falsified? The simple answer is that there has not been even an attempt to do so.This lack of defining even a falsifiable trait limits Darwinism to a philosophy,and you have in fact acknowledged that.

Gavin » Fri Nov 18, 2011 5:17 pm…. The thought of a purely naturalistic, purposeless origin for everything also seems to be very comforting to me. But then I'm quite irresponsible - if there's no cosmic purpose, then I'm off the hook for pulling my weight.

You now appear to be trying to row back from your own statement of belief by suggesting that the verifiable evidence I have produced is only a product of my belief.

Your description of what is science, does deserve a comment. You might find these descriptions of science helpful.

Science alone of all the subjects contains within itself the lesson of the danger of belief in the infallibility of the greatest teachers in the preceeding generation . . .As a matter of fact, I can also define science another way: Science is the belief in the ignorance of experts. Richard Feynman, Nobel-prize-winning physicist, in The Pleasure of Finding Things Out as quoted in American Scientist v. 87, p. 462 (1999).

scottie wrote:But trying to move the goal posts into the philosophical area won’t work, and for this reason.

The goal posts are already philosophical. I haven't moved them.

scottie wrote:Every one is aware that functional design (whether good, or not so good or even downright bad) displays itself with certain properties.1) The function has a purpose. ( i.e. It goes from A to B with C as it’s goal )2) Method by which that purpose is achieved. (How does it go from A to B)3) It would not contain parts or units that had no function toward the purpose.

Why should these properties be limited to design?

scottie wrote:Now you tried to falsify and failed with the phylogenetic data and tree building.. argument

I don't recall having failed. I think I said something like evolution being falsified if phylogenetic trees could not be built, and you resorted to the creationist Cambrian argument, and I resorted to how science works and how an incomplete fossil record is not an observation. How does this constitute failure? Ignoring the myriad of trees that have been built from the available evidence is an example of how you are selectively discounting the available evidence that doesn't support your beliefs. Sure, the tree is not complete, but are the gaps in an otherwise rather impressive assemblage MORE LIKELY to represent disproof of the whole or an incomplete collection or availability of evidence?

scottie wrote:However where have you or indeed anyone even attempted to define how Darwinism could be falsified?

I think it was Jerry Coyne who said that he would abandon his belief in evolution if a human fossil were ever found in Cretaceous strata. This is just one of many proposed examples of how evolution could be falsified. Darwin also mentioned a few examples. The inability to build phylogenetic trees, that I proposed above but that you seem to have forgotten, is another.

scottie wrote:You now appear to be trying to row back from your own statement of belief by suggesting that the verifiable evidence I have produced is only a product of my belief.

I have only said that you are selectively cherry picking a small subset of the available evidence and discounting the larger subset. The cherry picking is a product of your belief, not the evidence.

scottie wrote:I particularly like Richard Feynman’s comment.

Science alone of all the subjects contains within itself the lesson of the danger of belief in the infallibility of the greatest teachers in the preceeding generation . . .As a matter of fact, I can also define science another way: Science is the belief in the ignorance of experts.

Feynman said lots of interesting things. He also said, "God was invented to explain mystery. God is always invented to explain those things that you do not understand. Now, when you finally discover how something works, you get some laws which you're taking away from God; you don't need him anymore. But you need him for the other mysteries. So therefore you leave him to create the universe because we haven't figured that out yet; you need him for understanding those things which you don't believe the laws will explain, such as consciousness, or why you only live to a certain length of time - life and death - stuff like that. God is always associated with those things that you do not understand."

scottie, you have not responded to this. And you know what I like most to do, right?

JackBean wrote:So far, although you were bullshitting with non-sense, I have respected you at least because you were stick with your opinion, no matter, how silly it may be. But I see, you are neglegting yourself already.

JackBean wrote:scottie, I'm sure you will first answer my very old question, right?

JackBean wrote:You have not again said, how did the humans appear on Earth. Try to read this carefully and pick one possibility (or come up with other, but do not start about lysosomes )1) they were created when all the other life on Earth was created few billions of years ago2) they were created few tens/hundreds thousands of years ago when the creator was bored again and had no forum to post on3) they evolved from lower animals, no matter, whether these were created or arose spontanneously

you said, that 1 and 3 are wrong, so the creator "arrived" several times on Earth and worked on schifts, right? That would at least explain, why we don't find fossils of recent animals in say Mesozoic era.

scottie wrote:Jackbean

The No 2 option of yours is the nearest to my view without of course the rather silly appendage you have attached.

Another thing you have not responded to:

JackBean wrote:The simple question is this.Is intelligent design actually supported by evidence or is it simply your belief that it is.

Since you require evidence for evolution, how is that, that you do not require one for ID?

scottie wrote:

Right, they are all wrong, all the evolutionists, all IDers and all creators are wrong, but one retired engineer with no biological knowledge is right

My major point seems to have escaped your understanding.

If evolutionary theory (in all it’s various forms) is correct then there will be no disagreement between the theorists as to what the mechanism that drives macro evolution actually is.The reality that different dissenting views not only exist but are actually competing for prominence demonstrates that the mechanism is not known.The only common thread that unites the various adherents is that a naturalistic cause is the only one that is acceptable, regardless of where the evidence leads.

This makes any of these theories philosophically based. That is not a view I have any difficulty with, other than the point that it is regarded as a scientific fact and any dissension from that view is regarded as intolerable and therefore worthy of censorship, as you yourself have so plainly demonstrated.

Imagine, that we are able to travel in time and transfer say a car into medieval times. They will try to explain, how the car functions, but none of them will be probably right, since they don't have enough knowledge. Does that mean that the car doesn't work?